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TENSOR2 Volume II - Practical manual Patrice Dosset, Dominique Marion & Martin Blackledge
Institut de Biologie Structurale J.P. EBEL CEA-CNRS
Introduction Theory Whats New in TENSOR2 How to use TENSOR2. Material Required Running the Program Format of Input Files Visualisation Menu Selection of residues to be taken into account for determination of D or tau-c
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Inertia Tensor Selection of the spectrometer frequency Selection of the angle between csa and dipolar interactions Fit of relaxation data using isotropic tensor. Simple Fit Error Calculation and Confidence limit testing Fit of relaxation data using Anisotropic tensor. Simple Fit Error Calculation and Confidence limit testing Visualisation Diffusion Axes Display Axis Orientation Comparison of Inertia and Diffusion Tensors. Angular Dispersion Fully Asymmetric Model. Viewing Dispersion of Diffusion Tensor Axes. Viewing results of Monte-Carlo Simulations Specific Rotation
Internal Mobility Spectral density functions. Select Internal Mobility Mode Selection of sites to be fitted. Available models. Selection of Internuclear Distance NH. Selection of Specific Tau-c.
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Number of simulations to be performed for the Monte-Carlo analysis of Internal Mobility. Starting the Calculation. Graphical Representation of the Internal mobility Parameters. Inspection of {S2,ti} parametric space. Superposition of Internal Mobility Parameters onto the Protein Ribbon/Backbone. Output Coordinate Files Write coordinate file in Inertial Frame Write coordinate file in Diffusion Frame Postscript Output
Output Files resaniso.0 ( results of the fits, error calculations and validity tests ) : resaniso.1 ( Resultats of Monte-Carlo simulations ) : Introduction We present the program TENSOR2, which allows the determination of rotational diffusion from three-dimensional structure coordinates and experimental 15N relaxation data, and now, as mentioned below, allows a rigorous model-free analysi s of local internal mobility affecting backbone amides, from 15N {R1,R2,nOe} relaxation rates in the presence of an isotropic of anisotropic rotational diffusion tensor. Confidence in the various models available to describe the tensors and the internal mobility parameters are estimated using Monte-Carlo sampling methods in combination with appropriate χ2 and F-tests, made possible by a highly efficient simulated annealing algorithm. A graphical interface allows the visualisation of the orientation of tensorial components with respect to the three-dimensional coordinates of the molecule, and provides a presentation of the statistical behaviour of the system.
What's New in Tensor Version 2.0? Firstly and most importantly, Tensor2 now carries out an analysis of internal motion using the Lipari-Szabo or extended Lipari-Szabo type analysis. It's about time. This can either be performed using an isotropic rotor to describe rotational diffusion, or using the anisotropic tensor determined using a subset of spins, themselves assumed to have a negligible component to their internal motion. The internal mobility analysis is performed using the logic introduced by the NIH lab (Clore et al 1990), and reproduced by Professor Art Palmer's lab
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(Mandel et al 1995), sequentially fitting with more complicated models until the data are adequately reproduced. The confidence limits and uncertainty in the parameters are determined using a rapid monte-carlo based statistical analysis. As has been noted by numerous authors, the error function defined by the fitted internal mobility parameters {S2,ti} is highly non-linear when fitting R1,R2 and heteronuclear nOe. It is now possible to rapidly scan the monte-carlo simulations from the fit of each 15N site to check the definition of the optimised internal mobility parameters. The program also has undergone a large number of cosmetic improvements (ribbon and ball-and-stick display options) and the local motion can now be indicated using colour scales on the molecule. Interactive residue-identification using the cursor aids in recognising more or less mobile parts of the molecule.
How to use TENSOR. Material Required. The program has been compiled for the following platforms -
1. 2. 3. 4.
Silicon Graphics running Unix 6.5 or higher. Sun Sparc PC Linux : for redhat 9.0 you will need openmotif-2.2.2-14 Mac OS X 10.2 or 10.3: you will need Apple's free X11 server and openmotif-2.2.0-OSX
Running the Program
- tensor2 [Relaxation-Data-File Coordinate-File] The name of the output files are For the Diffusion tensor analysis :anisores.0 for the results of the fit and anisores.1 for the results of the Monte-Carlo error analysis. For the Analysis of Internal Mobility : ?????
Format of Input Files.
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Relaxation Data : Example : 0 2 1.1407 0.043841 12.6434 0.28419 0.768764 0.014567 1 3 1.2425 0.033048 13.3264 0.20920 0.80534 0.023311 1 4 1.2274 0.029092 13.0570 0.16854 0.57453 0.045632 1 5 1.2125 0.055488 12.8067 0.20193 0.764352 0.067832 ......... The 1st column (optional) is a flag describing whether the residue should be taken into account in the fit or not. (if 0 the residue is not taken included in the error function). The 2nd column specifies the number of the resiude in the primary sequence. Columns 3 and 4 represent R1 and associated uncertainty (in s-1). Columns 5 and 6 represent R2 and associated uncertainty (in s-1). Columns 7 and 8 represent the heteronulcear nOe and associated uncertainty (no units) - these are not necessary (and can be left out) if no analysis of internal mobility is to be performed. Coordinate File : The coordinate file is a standard .pdb file
Visualisation Menu. When the prgram is opened the molecule hree dimensional coordinates of the molecule are displayed, using one of diverse ribbon-type formats, backbone trace, ball-and-stick or stick representations chosen in the Stylemenu Atoms are coloured according to atom type.
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The display shows the three-dimensional coordinates of the N atoms from the input file. Note that the molecule can be rotated about x, y and z using the left and ( right mouse button or click with the left mouse button while holding down the Shift key ). If the molecule is dimeric, either or both monomers can be selected for display usingthe button on the right. The individual atoms or residues of the molecule can be identified using the Select button botton left of the display, and the identification mode button (Residue-name, atom-name ...).
In ribbon mode, individual residues can be displayed by clicking on the appropriate part of the ribbon.
Selection of residues to be taken into consideration for fitting overall diffusion/correlation time.
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Using the menu Visualisation-Definition the primary sequence will be displayed - from this the user can select the residues to be used in the fitting of the molecular diffusion. If the user had included a first column in the input-data file, the residues chosen wre already highlighted and are those which will be used. Otherwise to select resides, simply use the cursor and click Select or Unselect. The points above the letteres signify that there are R1,R2 data available for these residues. While selecting data to be incorporated into the fit, the user can visualise the molecule by clicking on the button 2nd Display.
Inertia Tensor. To calculate the inertia tensor, just click on Inertia Tensor :
The principal axes of the inertia tensor are shown in white. The inertia calculation is performed using the displayed molecular coordinates. In the case of a dimer this can be either monomer or the complete molecule.
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The relative moments are shown in the text window.
Selection of the spectrometer frequency:
The spectrometer frequency can be selected Spectrofrom the menu Setup. Select the 1H frequency using the list. The exact frequency of 1H et 15N can also be modified manually.
Selection of the angle between csa and dipolar interactions
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A common angle theta between the csa and dipolar interactions can be set using the option Csa from the menu Setup. The default value is 0°, that is the interactions are assumed to be coaxial as in the standard treatment.
Fit of relaxation data using isotropic tensor. In this case all directions are assumed equal and the contribution to rotational diffusion is independant of vector orientation. This is simply a fit of the average R2/R1 ratio to τc for those residues chosen in the selection procedure performed above. Simple Fit: Select Isotropy in the menu immediately underneath the main window (options -Anisotropy, Isotropy, Internal Mobility D-Iso, Internal Mobility D-Aniso). Click on Fit. This gives the following display of the average R2/R1 ratio with respect to overall correlation time, and the limits of the R2/R1 range.
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Error Calculation and Confidence limit testing : Specify the number of simulations for the Monte-Carlo procedure and click on Monte-Carlo. This calculation not only estimates the uncertainty in the overall correlation time determined from the selected residues, but also provides a measure of the confidence in the predicted value. The comparison with the simulated χ2 distribution allows you to decide whether isotropic tumbling is in fact applicable to your molecular system. In the case shown below such a model is rejected using 95% confidence limits, as the experimental χ 2 (whose value is shown as the yellow line) is much higher than that simulated from the optimal correlation time (95% of simulated χ2values are lower than the orange line), assuming the experimental errors describe the random fluctuation of the measured relaxation rates.
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If this model is satisfactory, you can now go straight to the Internal Mobility analysis, using this correlation time to describe the overall tumbling in the Lipari-Szabo-type model-free analysis;
To do this simply click on the button currently displaying Isotropy, (immediately underneath the main window (options -Anisotropy, Isotropy, Internal Mobility D-Iso, Internal Mobility D-Aniso)) and select Internal-Mobility-D-Iso.
Fit of relaxation data using Anisotropic tensor. Simple Fit: To choose the anisotropic diffusion tensor click on the button immediately underneath the main window (options -Anisotropy, Isotropy, Internal Mobility D-Iso, Internal Mobility D-Aniso)) and select Anisotropy.
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Again the residues to be taken into consideration for the fit to the overall difusion tensor can be selected using the interactive graphical selection in Visualisation-Definition.
To perform the fit, using the selected data and molecular coordinates, click on Fit.
Error Calculation and Confidence limit testing : Specify the number of simulations for the Monte-Carlo procedure and click on Monte-Carlo.
Visualisation of Result Diffusion Axis Display The results of the fit can be visualised by selecting Diffusion Axis in the menu Visualisation. An example is shown below - Note that the user can again move the molecular orientation using the mouse to inspect the axis orientation. A grid representation can be added to facilitate visualisation ot the tensor.
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Axis Orientation. The different orientations can also be visualised using the Orientation option in the menu Visualisation. Dxx, Dyy and Dzz are shown in the same representation as above (blue axes). The unique axes of the prolate and oblate axially symmetric tensors are shown as the z-axis (coming out of the screen) in the centre and right hand panels of the top half of this representation and the molecule is oriented in the bottom panels such that the three axes Dxx, Dyy and Dzz are aligned perpendicular to the screen plane. Not surprisingly in the example shown, two of the axes of the fully anisotropic tensor coincide with the oblate and prolate axially symmetric tensors (Blackledge et al 1998, Cordier et al 1998).
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Comparison of Inertia and Diffusion Tensors. To compare the inertia tensor orientation with the diffusion tensor orientation, click on inert/diff :
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The angles between the respective axes are shown as white arcs, and their values are given in degrees.
Angular Dispersion. The dispersion of the experimental and calculated relaxation rate ratios can be visualised by selecting R1/R2Alpha in the menu Visualisation. As shown for the example below, the data (centred on the error bars) can be compared to the optimal dispersion calculated from the best-fit tensor for this model (yellow points). A graphical logo is used to remind the user which of the dispersions is characteristic of an oblate and which of a prolate tensor.
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The range of α is shown from 0° to 180°, although orientations of α and (π−α) relative to the unique axis of the tensor are of course equivalent.
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Fully Asymmetric Model. The experimental relaxation rate ratios and those expected from a fully asymmetric diffusion tensor can be visualised with respect to the protein sequence by selecting R1/R2Back in the menu Visualisation. Again the data (centred on the error bars) can be compared to the optimal values calculated from the best-fit tensor for this model (yellow points).
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Viewing Dispersion of Diffusion Tensor Axes. The dispersion in the directions of the axes of the diffusion tensor, due to experimental uncertainty, is calculated directly from Monte Carlo simulations and can be viewed by selecting the Dispersion button. This gives an idea of the accuracy available from the relaxation measurements. The three axis orientations are shown as points around the three optimal axes which are shown as solid lines.
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Below is a second example where the tensor is an axially symmetric prolate rotor - note that the perpendicular components are degenerate and their orientation ill-defined, while the direction of the unique axis (Dzz) is well defined. This example show quite clearly the redundancy of axially symmetric tensorial models - if the tensor is axially symmetric, and there is absolutely no reason why it should be - this will be obvious from the analysis of the dispersion of the tensor components in the plane perpendicular to the uniqiue axes. As mentioned in the Theory part of this documentation, we feel that the axially symmetric model is a meaningless approximation, which, due to its dual-definition with two minima for the prolate and oblate approximations, is very difficult to test statistically, and brings no significant improvement to the data analysis. If in doubt, ask a solid state nmr spectroscopist why she/he doesn`t assume csa tensors to be axially symmetric to simplify their analysis.
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Viewing results of Monte-Carlo Simulations : Nevertheless, to satisfy demand, we retain the analysis using axially symmetric models, for the diffusion tensors. The statistical analysis performed using the Monte-Carlo function can be viewed by selecting Monte_Carlo in the menu Visualisation.
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The results of four calculations are summarised in these plots. 1. The top left-hand figure shows the χ2 distribution for the Monte-Carlo simulations for the first axially symmetric tensorial model (that with the lowest experimental χ2). 2. The bottom left-hand figure shows the χ2 distribution for the Monte-Carlo simulations for the second axially symmetric tensorial model (that with the higher experimental χ2). 3. The top right-hand figure shows the χ2 distribution for the Monte-Carlo simulations for the fully anisotropic tensorial model.
The explicitly simulated χ2 distributions are compared to the experimental fit and summarised using the following code : yellow : experimental χ2 blue : χ2 (0.10) orange : χ2 (0.05) If the experimental χ2 is higher than the simulated limits then the model cannot be used to
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explain the experimental data with acceptable confidence.
4. The bottom right-hand figure shows the comparison of simulated F-values (datasets from the best four-parameter fit fitted with 4 and 6 parameters to calculate the random statistical improvement due to the more complex fit) and the experimental improvement.
In this case yellow : experimental F blue : F (0.20) orange : F (0.10) If the experimental F is higher than the simulated limits then the improved fit found when using the more complex fit is above the random expected level and can be used with acceptable confidence.
Specific Rotation. Any Euler rotation of the diffusion tensor can be applied by entering specific euler angles using the menu Control - Rotation as shown -
Internal Mobility Spectral density functions Once the overall diffusion has been a determined, the program will perform a rigorous Lipari-Szabo type analysis of the internal mobility of the molecule using either the
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isotropic tensor as determined from the average R2/R1 ratio with the spectral density function of the form -
or using the anisotropic diffusion tensor resulting from the above analysis, with the analgous spectral density function -
where Ajare functions of the orientation of the vector to be analysed and τj are defined by Dxx,Dyy and Dzz.
Select Internal Mobility Mode To select the Internal Mobility mode of TENSOR2 click on the menu immediately underneath the main window (options -Anisotropy, Isotropy, Internal Mobility D-Iso, Internal Mobility D-Aniso) and select Internal Mobility D-Iso or Internal Mobility D-Aniso.
Selection of sites to be fitted.
Using the menu Definition the user can again select residues to be treated (this will often be all the molecule) by using the cursor to define the regions of the primary sequence to be included in the analysis.
Selection of Internuclear Distance NH. Our analysis of internal mobility assumes co-axial NH and axially symmetric csa tensor. the user can choose the internuclear distance from the menu Control DistanceNH, from 1.01 to 1.05Å.
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Selection of Specific Tau-c. The user can define a tau-c, different from the one fitted using the average R2/R1, from the menu Control - Tc (in units of seconds).
Available models. Dynamic Parameters Model 1 Model 2
,
Model 3
,
Model 4
, ,
Model 5
,
, =
The program will then test the models (1-5) shown above, (see theory) against the experimental {R1,R2,nOe} for each residue selected. Once the data can be reproduced satisfactorily from one of the models (as determined from Monte-Carlo simulations) the program selects this model and then goes onto the next residue. If one of the models (2 or 3) does not improve the fit enough to satisfy the F-test (α=0.2}, then the previously failed, but marginal, model 1 is accepted. If none of the models can reproduce the data satisfactorily the program will assign model 6 - this means that neither models 4 or 5 {3 parameters for 3 measureables} was sufficiently close to a 0 χ2 for the model to be acceptable. The mobility parameters for the best of these models are nevertheless given in the final table.
Number of simulations to be performed for the Monte-Carlo analysis of Internal Mobility. This is controlled by entering the required number (per model per residue, so this governs how long the calculation will take) in the window Nb Cycles.
Starting the Calculation. Once these parameters have been set the calculation can be started using the button Start-Mobility.
Graphical Representation of the Internal mobility Parameters.
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Once the calculation is finished, the user can inspect the fits graphically from the menu Visualisation - Mobility. This gives bar charts of all of the internal mobility parameters and the optimal models for each dataset.
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Each of these can be inspected in detail using the Visualisation-Mobility menu, and the position of the cursor in the primary sequence can be highlighted using the 2nd View option.
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Inspection of {S2,ti} parametric space. For those sites fitted using a model {2,4 ,5} that is with {S2,τi}, the error function samples by the Monte-Calro simulations can be inspected to check for anomalies, out-liers or double mimima (can be a problem for shorter τc) . This is again available in the Visualisation-Mobility menu (S2/ti). Note that in the case of outliers, the user can cheat, by changing the limits for the calculation of the uncertainty in tau-i by sliding the red-error limits from each side of the window - use with care!
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Superposition of Internal Mobility Parameters onto the Protein Ribbon/Backbone.
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Using the Visualisation View-Molecule menu, the user can colour the different ball-and-stick, stick, backbone or ribbon representations of the molecule using the order parameter as a scale to visualise differential mobility.
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Output Coordinate Files Write coordinate file in Inertial Frame ( menu File -> Save PDB file in Inertial Frame )
The coordinates of the displayed molecule can be written in the inertial frame (Cartesian x,y and z are aligned along Ix, Iy and Iz) using the File menu .
Write coordinate file in Diffusion Frame ( menu File -> Save PDB file in Diffusion Frame )
The coordinates of the displayed molecule can also be written in the diffusion frame (Cartesian x,y and z are aligned along Dxx, Dyy and Dzz) using the File menu .
Postscript Output Postscript files of each of the available displays can be saved or printed using the Menu : Print-Graph option.
Output Files - Results 30 of 34
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Text files iso.0 and iso.1 and resaniso.0 and resaniso.1 containing details of the different fits and Monte Carlo simulations can be saved or printed using the Menu : Print-Result option.
resaniso.0 ( results of the fits, error calculations and validity tests ): Full Asymmetry : Chi2
Alpha
Beta
Gamma
Dx
Dy
Dz
3.8545e+01 -> 6.6733e+01 7.5621e+01 7.7959e+01 1.4079e-01 1.5660e-01 1.8301e-01
Axial Symmetry ( 1st min ) : Chi2
Phi
4.4357e+01 -> -2.9704e+01
Teta
DPer
Dpar
2.0094e+01 1.6992e-01 1.4323e-01
Axial Symmetry ( 2nd min ) : Chi2
Phi
Teta
4.4646e+01 -> 7.8328e+01 7.2317e+01
DPer 1.4410e-01
Dpar 1.9258e-01
***************************************************************************
Number of simulations : 500
Axial Symmetry 1st Minimum Phi(deg.) : -29.704 -+ 4.770 Teta(deg.) : 20.094 -+ 10.735 Dper : 1.699e-01 -+ 1.101e-03 Dpar : 1.432e-01 -+ 2.292e-03 Chi2_Exp : 4.4357e+01 Chi2_Mc ( 0.10 ) : 5.0664e+01 Chi2_Mc ( 0.05 ) : 5.3855e+01 31 of 34
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0.10 Chi2 Montecarlo Aniso. Ax. ( 5.0664e+01 ) > Chi2exp ( 4.4357e+01 ) : --> Accepted Model 0.05 Chi2 Montecarlo Aniso. Ax. ( 5.3855e+01 ) > Chi2exp ( 4.4357e+01 ) : --> Accepted Model
Axial Symmetry 2nd Minimum Phi(deg.) : 78.329 -+ 3.001 Teta(deg.) : 72.316 -+ 3.893 Dper : 1.441e-01 -+ 2.309e-03 Dpar : 1.926e-01 -+ 3.808e-03 Chi2_Exp : 4.4646e+01 Chi2_Mc ( 0.10 ) : 5.0941e+01 Chi2_Mc ( 0.05 ) : 5.3802e+01 0.10 Chi2 Montecarlo Aniso. Ax. ( 5.0941e+01 ) > Chi2exp ( 4.4646e+01 ) : --> Accepted Model 0.05 Chi2 Montecarlo Aniso. Ax. ( 5.3802e+01 ) > Chi2exp ( 4.4646e+01 ) : --> Accepted Model
Full Asymmetry Alpha(deg.) : 66.733 -+ 8.861 Beta(deg.) : 75.621 -+ 3.526 Gamma(deg.) : 77.959 -+ 9.020 Dx : 1.408e-01 -+ 2.698e-03 Dy : 1.566e-01 -+ 4.878e-03 Dz : 1.830e-01 -+ 4.947e-03 Chi2_Exp : 3.8545e+01 Chi2_Mc ( 0.10 ) : 4.8427e+01 Chi2_Mc ( 0.05 ) : 5.2107e+01 0.10 Chi2 Montecarlo Aniso. Tot. ( 4.8427e+01 ) > Chi2exp ( 3.8545e+01 ) : --> Accepted Model 0.05 Chi2 Montecarlo Aniso. Tot. ( 5.2107e+01 ) > Chi2exp ( 3.8545e+01 ) : --> Accepted Model
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Fexp = 2.8646e+00 ( P = 6.9377e-02 ) Fexp > 0.2 FTest ( 1.7549e+00 ) : Significant Improvement Fexp > 0.1 FTest ( 2.5394e+00 ) : Significant Improvement
resaniso.1 ( Resultats of Monte-Carlo simulations ) :
Monte_carlo Axial Symmetry 1st min ... Chi2
Phi
Teta
0 McTotal4_1 : 3.0864e+01 -> -3.8505e+01 1 McTotal4_1 : 3.4538e+01 -> -2.3209e+01 2 McTotal4_1 : 3.4669e+01 -> -2.9521e+01 3 McTotal4_1 : 3.5939e+01 -> -3.4292e+01 ......
4.7903e+01 8.1993e+00 1.2921e+01 2.5437e+01
DPer 1.7136e-01 1.7078e-01 1.6937e-01 1.7108e-01
Dpar 1.3968e-01 1.4047e-01 1.4394e-01 1.4188e-01
Monte_carlo Axial Symmetry 2nd min ... Chi2
Phi
Teta
0 McTotal4_2 : 3.3527e+01 -> 6.8408e+01 1 McTotal4_2 : 3.3805e+01 -> 7.9317e+01 2 McTotal4_2 : 3.4567e+01 -> 8.2116e+01 3 McTotal4_2 : 3.5743e+01 -> 7.5627e+01 ......
7.2778e+01 7.2583e+01 7.1891e+01 7.1596e+01
DPer
Dpar
1.4723e-01 1.4144e-01 1.4027e-01 1.4403e-01
1.8727e-01 1.9637e-01 1.9930e-01 1.9361e-01
Monte_carlo Full Asymmetry ...
Dyy
Chi2 Dzz
Alpha
Beta
Gamma
Dxx
0 McTotal6 : 2.9449e+01 -> 6.8753e+01 6.3743e+01 8.7595e+01 1.3859e-01 1.6400e-01 1.7773e-01 1 McTotal6 : 3.1338e+01 -> 6.4532e+01 7.8114e+01 7.4422e+01 1.4017e-01 1.4735e-01 1.9140e-01 2 McTotal6 : 3.3729e+01 -> 7.2315e+01 8.0004e+01 7.7963e+01 1.3652e-01 1.5369e-01 1.8833e-01 3 McTotal6 : 3.5382e+01 -> 6.3496e+01 7.2177e+01 7.5137e+01 1.4078e-01 1.5703e-01 1.8393e-01 33 of 34
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......
References. Woessner, D. E. J.Chem.Phys. 1962, 37, 647-654. Blackledge, M.; Cordier, F.; Dosset, P.; Marion, D. J.Am.Chem.Soc. 1998, 120, 4538-4539. Cordier, F.; Caffrey, M.; Brutscher, B; Cusanovich, M.; Marion, D.; Blackledge, M. J.Mol.Biol. 1998, 281, 341-361. Efficient analysis of macromolecular rotational diffusion from heteronuclear relaxation data. Dosset, P.; Hus, J-C; Blackledge, M.; Marion, D. J.Biomol.NMR. 2000, 16: 23-28. Rotational diffusion anisotropy and local backbone dynamics of carbon monoxide bound Rhodobacter capsulatus cytochrome c'. Tsan, P.; Hus, J-C; Caffrey, M. ; Marion. D. & Blackledge, M. J.Am.Chem.Soc. 2000, 121,2311-2312.
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